Mutations in iron-sulfur cluster proteins that improve xylose utilization

ABSTRACT

There is provided an engineered host cells comprising (a) one or more mutations in one or more endogenous genes encoding a protein associated with iron metabolism; and (b) at least one gene encoding a polypeptide having xylose isomerase activity, and methods of their use thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 15/884,449 filedJan. 31, 2018, which is a continuation of U.S. Ser. No. 14/821,955 filedAug. 10, 2015, now U.S. Pat. No. 9,920,312, which claims priority fromU.S. provisional application 62/035,748 filed on Aug. 11, 2014, thecontents of each of which are incorporated by reference in theirentirety.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was funded, in part, by the United States governmentunder a grant with the Department of Energy, Office of Energy Efficiencyand Renewable Energy, Bioenergy Technologies Office, Award No.DE-FC36-08GO18103 to Mascoma and FWP#CEEB007 to Oak Ridge NationalLaboratory. This invention was also funded, in part, by the BioenergyScience Center, Oak Ridge National Laboratory, a U.S. Department ofEnergy Bioenergy Research Center supported by the Office of Biologicaland Environmental Research, under contract DE-PS02-06ER64304. Thegovernment has certain rights in the invention.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY VIA EFS-WEB

The contents of the attached sequence listing (named115235-264-seq_listing.txt; of size 112 kb, created Sep. 17, 2019) areincorporated by reference in their entirety.

FIELD OF THE INVENTION

The field of the invention generally relates to engineered host cellscomprising (a) one or more mutations in one or more endogenous genesencoding a protein associated with iron metabolism; and (b) at least onegene encoding a polypeptide having xylose isomerase activity; andmethods of fermenting cellulosic biomass to produce biofuels, includingethanol.

BACKGROUND OF THE INVENTION

Saccharomyces cerevisiae is the primary biocatalyst used in thecommercial production of “first generation” fuel ethanol from sugarbased substrates such as corn, sugarcane, and sugarbeet. Secondgeneration ethanol production, also known as cellulosic ethanolproduction, extends the carbohydrate source to more complexpolysaccharides, such as cellulose and hemicellulose, which make up asignificant portion of most plant cell walls and therefore most plantmaterial.

Feedstocks commercially considered for second generation ethanolproduction include wood, agriculture residues such as corn stover andwheat straw, sugarcane bagasse and purpose grown materials such asswitchgrass. The cellulose and hemicellose must be hydrolyzed tomonomeric sugars before fermentation using either mechanical/chemicalmeans and/or enzymatic hydrolysis. The liberated monomeric sugarsinclude glucose, xylose, galactose, mannose, and arabinose with glucoseand xylose constituting more than 75% of the monomeric sugars in mostfeedstocks. For cellulosic ethanol production to be economically viableand compete with first generation ethanol, the biocatalyst must be ableto convert the majority, if not all, of the available sugars intoethanol.

S. cerevisiae is the preferred organism for first generation ethanolproduction due to its robustness, high yield, and many years of safeuse. However, naturally occurring S. cerevisiae is unable to fermentxylose into ethanol. For S. cerevisiae to be a viable biocatalyst forsecond generation ethanol production, it must be able to ferment xylose.

There are two metabolic pathways of xylose fermentation that have beendemonstrated in S. cerevisiae. The pathways differ primarily in theconversion of xylose to xylulose. In the first pathway, the XR-XDHpathway, a xylose reductase (XR) converts xylose to xylitol, which issubsequently converted to xylulose by a xylitol dehydrogenase (XDH). TheXR and XDH enzyme pairs tested to date differ in required cofactor, NADHand NADPH, leading to difficulties achieving redox balance. The secondcommonly tried pathway converts xylose directly to xylulose using axylose isomerase (XI) with no redox cofactor requirements. XIs from bothbacterial and fungal systems have been successfully utilized in S.cerevisiae. Both pathways utilize the same downstream metabolicengineering: up regulation of the native xylulose kinase (XKS1) and fourgenes of the pentose phosphate pathway, specifically ribulose-phosphate3-epimerase (RPE1), ribose-5-phosphate ketol-isomerase (RKI1),transaldolase (TAL1), and transketolase (TKL1) (FIG. 1). Use of the XIpathway also commonly entails deletion of the native aldose reductasegene (GRE3) to eliminate product lost to xylitol formation.

Xylose isomerases are known to have several metal ion binding sites,which allows XIs to bind metal ions such as manganese, cobalt, andmagnesium. See, e.g., Chang et al., “Crystal Structures of ThermostableXylose Isomerases from Thermus caldophilus and Thermus thermophilus:Possible Structural Determinants of Thermostability,” J. Mol. Biol288:623-34 (1999). There is some indication that XIs may also bind ironcations (Fe+), but Fe+ is usually not the preferred or optimal divalentcation. However, intracellular iron regulation and metabolism is knownto be a critical function for eukaryotic cells due to iron's role as aredox-active protein cofactor. See, e.g., Outten and Albetel, “Ironsensing and regulation in Saccharomyces cerevisiae: Ironing out themechanistic details,” Curr. Op. Microbiol. 16:662-68 (2013).Intracellular iron levels are primarily controlled by the iron-sensingtranscriptional activators Aft1 and Aft2 in S. cerevisiae. Iron-sulfur(Fe/S) clusters are essential for transcriptional control by Aft1/2 andYap5 during iron sufficiency. Under sufficient iron levels, Fe/Sclusters are synthesized in the mitochondria through the integration ofiron, sulfur, and redox control pathways. The Fe/S clusters interactwith Grx3, Grx4, Fra1, and Fra2 to inactivate Aft1/2, leading to downregulation of Aft1/2 target genes. Fe/S clusters also are known toactivate the expression of Yap5 target genes, including CCC1. Ccc1stimulates the import of iron and its sequestration in the vacuole.

BRIEF SUMMARY OF THE INVENTION

Aspects of the invention are directed to engineered host cellscomprising (a) one or more mutations in one or more endogenous genesencoding a protein associated with iron metabolism; and (b) at least onegene encoding a polypeptide having xylose isomerase activity, andmethods of their use are described herein.

In some embodiments, the host cell heterologously expresses one or morepolypeptides capable of converting xylose to xylulose. In someembodiments, the one or more heterologously expressed polypeptide is axylose isomerase. In some embodiments, the heterologously expressedpolypeptide is a naturally occurring polypeptide. In some embodiments,the heterologously expressed polypeptide is recombinant. In someembodiments, the heterologously expressed polypeptide is a chimericpolypeptide. In some embodiments, the chimeric polypeptide is asdescribed in the related provisional application U.S. 62/035,752 filedon Aug. 11, 2014, which application is hereby incorporated by referencein its entirety.

In some embodiments of the present invention, the heterologouslyexpressed polypeptide has at least 80%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% sequence identity with any oneof SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and/or 27.In some embodiments, the heterologously expressed polypeptide has anamino acid sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19,21, 23, 25, or 27. In some embodiments of the present invention, theheterologously expressed polypeptide has at least 80%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% sequence identitywith any one of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23,25, 27, 35, 37, 39, and/or 41. In some embodiments, the heterologouslyexpressed polypeptide has an amino acid sequence of SEQ ID NOs: 1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, or 41.

In some embodiments, the heterologously expressed polypeptide is encodedby a polynucleotide sequence having at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 76%, at least77%, at least 78%, at least 79%, at least 80%, at least 81%, at least82%, at least 83%, at least 84%, at least 85%, at least 86%, at least87%, at least 88%, at least 89%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% sequence identity with any one of SEQID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and/or 28. Insome embodiments, the heterologously expressed polypeptide is encoded bya polynucleotide sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18,20, 22, 24, 26, or 28. In some embodiments, the heterologously expressedpolypeptide is encoded by a polynucleotide sequence having at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 76%, at least 77%, at least 78%, at least 79%, at least 80%, atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% sequence identitywith any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, 28, 36, 38, 40, and/or 42. In some embodiments, the heterologouslyexpressed polypeptide is encoded by a polynucleotide sequence of SEQ IDNOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, or42. In some embodiments, the polynucleotide sequence is contained in avector.

In some embodiments, a host cell is engineered to express one or more ofthe chimeric polypeptides. In some embodiments, the host cell is a yeastcell, e.g. a S. cerevisiae cell. In some embodiments the host cell isfurther modified to have mutations affecting at least one gene encodinga protein involved in the pentose phosphate pathway. In someembodiments, the host cell has at least one mutation that increases theexpression or causes the up-regulation of XKS1, RKI1, RPE1, TKL1, and/orTALL In some embodiments, the host cell has a modification of one ormore aldose reductase genes. In some embodiments, the aldose reductasegene is GRE3. In some embodiments, the host cell has a deletion ordisruption of all or part of the endogenous GRE3 gene. In someembodiments, the aldose reductase gene is YPR1. In some embodiments, thehost cell has a deletion or disruption of all or part of the endogenousYPR1 gene. In some embodiments, the host cell has a deletion ordisruption of all or part of both the endogenous GRE3 gene and theendogenous YPR1 gene. In some embodiments, the host cell has amodification of PGM1 (phosphoglucomutase 1) and/or PGM2. In someembodiments, the host cell overexpresses PGM1 and/or PGM2. In someembodiments, the host cell has increased levels of Pgm1 and/or Pgm2polypeptide and/or mRNA relative to a comparable host cell lacking amodification of PGM1 and/or PGM2.

In some embodiments, the host cell comprises a deletion or disruption ofone or more endogenous enzymes that function to produce glycerol and/orregulate glycerol synthesis. In some embodiments, the host cell producesless glycerol than a control recombinant microorganism without deletionor disruption of said one or more endogenous enzymes that function toproduce glycerol and/or regulate glycerol synthesis. In someembodiments, the one or more endogenous enzymes that function to produceglycerol are encoded by a GPD1 polynucleotide, a GPD2 polynucleotide, orboth a GPD1 polynucleotide and a GPD2 polynucleotide. In someembodiments, one or both of the endogenous GPD1 and/or GPD2 genes aremodified by mutation or deletion. In some embodiments, the host cellcomprises a heterologous ADHE sequence. In some embodiments, theheterologous ADHE is from Bifidobacterium adolescentis. In someembodiments the native STL1 gene is upregulated by either modifying thepromoter of the native copies or by introducing additional copies ofSTL1. In some embodiments the host cell comprises an ortholog of thenative STL1. In some embodiments the native ACS2 gene is upregulated byeither modifying the promoter of the native copies or by introducingadditional copies of ACS2. In some embodiments the host cell comprisesan ortholog of the native ACS2 or ACS1 gene.

In some embodiments, the host cell comprises one or more mutations inone or more endogenous genes encoding a protein associated with ironmetabolism. In some embodiments, the host cell comprises one or moremutations in one or more endogenous genes encoding an iron uptakeprotein, iron utilization protein, and/or an iron/sulfur (Fe/S) clusterbiosynthesis protein. In some embodiments, the host cell comprises oneor more mutations in one or more endogenous genes encoding a polypeptideaffecting iron metabolism or Fe/S cluster biosynthesis. In someembodiments, the host cell is a recombinant yeast cell. In someembodiments, the recombinant yeast cell comprises one or more mutationsin one or more of an endogenous gene selected from the group ISU1, YFH1,NFS1, AFT1, AFT2, YAP5, FRA1, FRA2, GREX3, GREX4, CCC1, and combinationsthereof. In some embodiments, the recombinant yeast cell comprises oneor more mutations in one or more of an endogenous gene which ishomologous to one or more of an S. cerevisiae gene selected from thegroup ISU1, YFH1, NFS1, AFT1, AFT2, YAP5, FRA1, FRA2, GREX3, GREX4, andCCC1. In some embodiments, the recombinant yeast cell comprises amutation in the endogenous AFT1 or AFT2 gene that results iniron-independent activation of the iron regulon such as the AFT1-1^(up)or AFT2-1^(up) alleles (Rutherford et al., “Aft1p and Aft2p mediateiron-responsive gene expression in yeast through related promoterelements,” JBC 278(30):27636-43 (2003)). In some embodiments, therecombinant yeast cell comprises a deletion or disruption of YAP5 and/orCCC1. In some embodiments, the recombinant yeast cell comprises adeletion or disruption of YAP5 and/or CCC1 and/or a mutation in theendogenous AFT1 or AFT2 gene that results in iron-independent activationof the iron regulon such as the AFT1-1^(up) or AFT2-1^(up) alleles.

In some embodiments, the host cell comprises one or more mutations inthe endogenous ISU1 gene that results in a polypeptide comprising atleast one amino acid substitution selected from the group consisting ofD71N, D71G, and S98F, wherein the position of the substitution isrelative to the amino acid positions of SEQ ID NO:29. In someembodiments, the host cell comprises one or more mutations in theendogenous YFH1 gene that results in a polypeptide comprising a T163Psubstitution, wherein the position of the substitution is relative tothe amino acid positions of SEQ ID NO:31. In some embodiments, the hostcell comprises one or more mutations in the endogenous NFS1 gene thatresults in a polypeptide comprising at least one amino acid substitutionselected from the group consisting of L115W and E458D, wherein theposition of the substitution is relative to the amino acid positions ofSEQ ID NO:33.

In some embodiments, the host cell has a modification of PGM1(phosphoglucomutase 1) and/or PGM2, as described in the relatedprovisional application filed on Aug. 11, 2014, which application isincorporated by reference in its entirety. In some embodiments, the hostcell overexpresses PGM1 and/or PGM2. In some embodiments, the host cellhas increased levels of Pgm1 and/or Pgm2 polypeptide and/or mRNArelative to a comparable host cell lacking a modification of PGM1 and/orPGM2.

In some embodiments, the host cell expresses one or more heterologousgenes encoding a protein that is associated with iron metabolism. Insome embodiments, the heterologous gene confers on the recombinant yeastcell an increased ability to utilize xylose as compared to a similaryeast cell lacking the heterologous gene. In some embodiments, theheterologous gene is AFT1, AFT2, and/or an orthologue thereof. In someembodiments, the heterologous gene encodes a polypeptide having irontransport activity. In some embodiments, the heterologous gene encodes aprotein that increases the activity and/or expression of Aft1 and/orAft2. In some embodiments, the heterologous gene is a target of Aft1and/or Aft2. In some embodiments, the heterologous gene isconstitutively expressed. In some embodiments, the heterologous gene isoverexpressed. In some embodiments, the heterologous gene encodes aprotein that suppresses a gene or protein that suppresses Aft1 and/orAft2 activity and/or expression. In some embodiments, the heterologousgene encodes a protein that suppresses a gene or protein that suppressesthe activity and/or expression of one or more downstream targets of Aft1and/or Aft2.

In some embodiments, a yeast strain is used as the host cell. In someembodiments, the background of the yeast strain is an industrial yeaststrain. One having ordinary skill in the art would be aware of manypotential known yeast strains that can be modified according to thepresent invention, and this invention contemplates all such potentialbackground yeast strains.

In some embodiments of the invention, the recombinant host cell is usedto produce a fermentation product from a cellulosic or lignocellulosicmaterial. In some embodiments, the fermentation product is ethanol,lactic acid, 3-hydroxy-propionic acid, hydrogen, butyric acid, acrylicacid, acetic acid, succinic acid, citric acid, malic acid, fumaric acid,an amino acid, 1,3-propane-diol, ethylene, glycerol, acetone, isopropylalcohol, butanol, a β-lactam, an antibiotic, a cephalosporin, or acombination thereof. In some embodiments, the cellulosic orlignocellulosic material is insoluble cellulose, crystalline cellulose,pretreated hardwood, paper sludge, pretreated corn stover, pretreatedsugar cane bagasse, pretreated corn cobs, pretreated switchgrass,pretreated municipal solid waste, pretreated distiller's dried grains,pretreated wheat straw, corn fiber, agave, or a combination thereof.

One aspect of the invention is directed to a composition comprising alignocellulosic material and a recombinant yeast host cell comprisingone or more mutations in one or more endogenous genes encoding a proteinassociated with iron metabolism and at least one gene encoding apolypeptide having xylose isomerase activity. Another aspect of theinvention is directed to a media supernatant generated by incubating arecombinant yeast host comprising one or more mutations in one or moreendogenous genes encoding a protein associated with iron metabolism andat least one gene encoding a polypeptide having xylose isomeraseactivity with a medium containing xylose as the only carbon source. Insome embodiments, the medium comprises a cellulosic or lignocellulosicmaterial. In some embodiments, the cellulosic or lignocellulosicmaterial is insoluble cellulose, crystalline cellulose, pretreatedhardwood, paper sludge, saw mill or paper mill discards, pretreated cornstover, pretreated sugar cane bagasse, pretreated corn cobs, pretreatedswitchgrass, pretreated municipal solid waste, pretreated distiller'sdried grains, pretreated wheat straw, corn fiber, agave, or acombination thereof.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES

FIG. 1 depicts a schematic representation of xylose fermentation ingenetically engineered S. cerevisiae.

FIG. 2 depicts a schematic representation of the role of Fe/S clustersin intracellular iron metabolism. See Outten and Albetel, “Iron sensingand regulation in Saccharomyces cerevisiae: Ironing out the mechanisticdetails,” Curr. Op. Microbiol. 16:662-68 (2013).

FIGS. 3A-3C provide examples of the relative growth of xylose utilizingyeast strains (XUS) with various mutations in genes encoding proteinsassociated with intracellular iron metabolism, specifically YFH1 (FIG.3A), ISU1 (FIG. 3B), and NFS1 (FIG. 3C).

FIGS. 4A-4B provide examples of the relative growth of xylose utilizingyeast strains (XUS) with heterozygous and homozygous mutations in genesencoding proteins associated with intracellular iron metabolism,specifically ISU1 (FIG. 4A) and ISU1 and YFH1 (FIG. 4B), in two XUSstrains.

FIG. 5 provides examples of the relative growth of xylose utilizingyeast strains heterologously expressing selected xylose isomerase genes,including those from B. thetaiotaomicron (BtXI), Piromyces (PiXI), C.aberensis (CaXI), P. ruminicola (PrXI), P. distasonis (PdXI), XYM2, A.defectiva (AdXI), Lachnoanaerobaculum saburreum (LsXI), Clostridiumphytofermentans (CpXI), and Lactobacillus xylosus (LxXI). The growthlevels for of each xylose utilizing yeast strain are show with (hashedbars) and without (solid bars) the T163P mutation of YFH1.

FIGS. 6A-6B provide examples of the relative growth of yeast cellsheterologously expressing selected xylose isomerases (chromosomallyintegrated) including those from CX355=chimeric xylose isomerase 355,CX1224=chimeric xylose isomerase 1224, Ad=Abiotrophia defectiva,Bt=Bacteroides thetaioatomicron, Pe=Piromyces, Ls=Lachnoanaerobaculumsaburreum with and without a mutation in YFH1. The growth levels for ofeach xylose utilizing yeast strain are show with (FIG. 6A) and without(FIG. 6B) the T163P mutation of YFH1.

FIG. 7 provides examples of the relative growth of xylose utilizingyeast strains (XUS) with various mutations in genes encoding proteinsassociated with intracellular iron metabolism, specifically AFT1, andccc1.

FIG. 8 provides examples of the relative ethanol production of xyloseutilizing yeast strains (XUS) grown in glucose/xylose media with andwithout iron addition

FIG. 9 provides examples of in vitro xylose isomerase activity assay ofxylose utilizing yeast strains (XUS).

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art of microbial metabolic engineering. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice of the disclosed methods and compositions, exemplarymethods, devices and materials are described herein.

The embodiment(s) described, and references in the specification to “oneembodiment”, “an embodiment”, “an example embodiment”, etc., indicatethat the embodiment(s) described can include a particular feature,structure, or characteristic, but every embodiment does not necessarilyinclude the particular feature, structure, or characteristic. Moreover,such phrases are not necessarily referring to the same embodiment.Further, when a particular feature, structure, or characteristic isdescribed in connection with an embodiment, it is understood that it iswithin the knowledge of one skilled in the art to effect such feature,structure, or characteristic in connection with other embodimentswhether or not explicitly described.

The description of “a” or “an” item herein refers to a single item ormultiple items. It is understood that wherever embodiments are describedherein with the language “comprising,” otherwise analogous embodimentsdescribed in terms of “consisting of and/or” consisting essentially ofare also provided. Thus, for example, reference to “a polynucleotide”includes a plurality of such polynucleotides and reference to “themicroorganism” includes reference to one or more microorganisms, and soforth.

A “fragment” refers to any portion of a nucleic or amino acid sequencethat is less than the entire sequence. A fragment of a nucleotide or anamino acid sequence can be any length of nucleotides or amino acids thatis less than the entire length of the cited sequence and more than twonucleotides or amino acids in length. In some embodiments, the fragmentcan be from a donor sequence.

A “vector,” e.g., a “plasmid” or “YAC” (yeast artificial chromosome)refers to an extrachromosomal element often carrying one or more genesthat are not part of the central metabolism of the cell, and can be inthe form of a linear or circular double-stranded DNA molecule. Vectorsand plasmids can be autonomously replicating sequences, genomeintegrating sequences, phage or nucleotide sequences, linear, circular,or supercoiled, of a single- or double-stranded DNA or RNA, derived fromany source, in which a number of nucleotide sequences have been joinedor recombined into a unique construction which is capable of introducinga promoter fragment and DNA sequence for a selected gene product alongwith appropriate 3′ untranslated sequence into a cell.

An “expression vector” is a vector that is capable of directing theexpression of genes to which it is operably associated.

The term “integrated” as used herein refers to genetic elements that areplaced, through molecular biology techniques, into the genome of a hostcell. For example, genetic elements can be placed into the chromosomesof the host cell as opposed to in a plasmid carried by the host cell.Methods for integrating genetic elements into the genome of a host cellare well known in the art and include homologous recombination. In someembodiments, more than one copy of the genetic elements are placed intothe genome of a host cell. In some embodiments, 2, 3, 4, 5, 6, 7, 8, 9,10, or more copies of the genetic elements are placed into the genome ofa host cell.

The term “heterologous” when used in reference to a polynucleotide, agene, a polypeptide, or an enzyme refers to a polynucleotide, gene,polypeptide, or an enzyme not normally found in the host organism.“Heterologous” also includes a native coding region, or portion thereof,that is removed from the source organism and subsequently reintroducedinto the source organism in a form that is different from thecorresponding native gene, e.g., not in its natural location in theorganism's genome. The heterologous polynucleotide or gene can beintroduced into the host organism by, e.g., gene transfer. Aheterologous gene can include a native coding region that is a portionof a chimeric gene including non-native regulatory regions that isreintroduced into the native host. Foreign genes can comprise nativegenes inserted into a non-native organism, or chimeric genes. Aheterologous polynucleotide, gene, polypeptide, or an enzyme can bederived from any source, e.g., eukaryotes, prokaryotes, viruses, orsynthetic polynucleotide fragments. The term “heterologous” as usedherein also refers to an element of a vector, plasmid or host cell thatis derived from a source other than the endogenous source. Thus, forexample, a heterologous sequence could be a sequence that is derivedfrom a different gene or plasmid from the same host, from a differentstrain of host cell, or from an organism of a different taxonomic group(e.g., different kingdom, phylum, class, order, family, genus, orspecies, or any subgroup within one of these classifications). The term“heterologous” is also used synonymously herein with the term“exogenous.” The term “heterologous expression” refers to the expressionof a heterologous polynucleotide or gene by a host.

The term “domain” as used herein refers to a part of a molecule orstructure that shares common physical or chemical features, for examplehydrophobic, polar, globular, helical domains or properties, e.g., a DNAbinding domain or an ATP binding domain. Domains can be identified bytheir homology to conserved structural or functional motifs. Examples ofcellobiohydrolase (CBH) domains include the catalytic domain (CD) andthe cellulose binding domain (CBD).

A “nucleic acid,” “polynucleotide,” or “nucleic acid molecule” is apolymeric compound comprised of covalently linked subunits callednucleotides. Nucleic acid includes polyribonucleic acid (RNA) andpolydeoxyribonucleic acid (DNA), both of which can be single-stranded ordouble-stranded. DNA includes cDNA, genomic DNA, synthetic DNA, andsemi-synthetic DNA.

An “isolated nucleic acid molecule” or “isolated nucleic acid fragment”refers to the phosphate ester polymeric form of ribonucleosides(adenosine, guanosine, uridine, or cytidine; “RNA molecules”) ordeoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, ordeoxycytidine; “DNA molecules”), or any phosphoester analogs thereof,such as phosphorothioates and thioesters, in either single strandedform, or a double-stranded helix. Double stranded DNA-DNA, DNA-RNA andRNA-RNA helices are possible. The term nucleic acid molecule, and inparticular DNA or RNA molecule, refers only to the primary and secondarystructure of the molecule, and does not limit it to any particulartertiary forms. Thus, this term includes double-stranded DNA found,inter alia, in linear or circular DNA molecules (e.g., restrictionfragments), plasmids, and chromosomes. In discussing the structure ofparticular double-stranded DNA molecules, sequences are described hereinaccording to the normal convention of giving only the sequence in the 5′to 3′ direction along the non-transcribed strand of DNA (i.e., thestrand having a sequence homologous to the mRNA).

A “gene” refers to an assembly of nucleotides that encode a polypeptide,and includes cDNA and genomic DNA nucleic acids. “Gene” also refers to anucleic acid fragment that expresses a specific protein, includingintervening sequences (introns) between individual coding segments(exons), as well as regulatory sequences preceding (5′ non-codingsequences) and following (3′ non-coding sequences) the coding sequence.“Native gene” refers to a gene as found in nature with its ownregulatory sequences. The terms “gene(s)” or “polynucleotide” or“nucleic acid” or “polynucleotide sequence(s)” are intended to includenucleic acid molecules, e.g., polynucleotides which include an openreading frame encoding a polypeptide, and can further include non-codingregulatory sequences, and introns. In addition, the terms are intendedto include one or more genes that map to a functional locus. Also, theterms are intended to include a specific gene for a selected purpose.The gene can be endogenous to the host cell or can be recombinantlyintroduced into the host cell, e.g., as a plasmid maintained episomallyor a plasmid (or fragment thereof) that is stably integrated into thegenome. In addition to the plasmid form, a gene can, for example, be inthe form of linear DNA or RNA. The term “gene” is also intended to referto multiple copies of a particular gene, e.g., all of the DNA sequencesin a cell encoding a particular gene product.

A nucleic acid molecule is “hybridizable” to another nucleic acidmolecule, such as a cDNA, genomic DNA, or RNA, when a single strandedform of the nucleic acid molecule can anneal to the other nucleic acidmolecule under the appropriate conditions of temperature and solutionionic strength. Hybridization and washing conditions are well known andexemplified, e.g., in Sambrook, J., Fritsch, E. F. and Maniatis, T.MOLECULAR CLONING: A LABORATORY MANUAL, Second Edition, Cold SpringHarbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter11 and Table 11.1 therein (hereinafter “Maniatis”, entirely incorporatedherein by reference). The conditions of temperature and ionic strengthdetermine the “stringency” of the hybridization. Stringency conditionscan be adjusted to screen for moderately similar fragments, such ashomologous sequences from distantly related organisms, to highly similarfragments, such as genes that duplicate functional enzymes from closelyrelated organisms. Post-hybridization washes determine stringencyconditions. One set of conditions uses a series of washes starting with6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with0.2×SSC, 0.5% SDS at 50° C. for 30 min. For more stringent conditions,washes are performed at higher temperatures in which the washes areidentical to those above except for the temperature of the final two 30min washes in 0.2×SSC, 0.5% SDS are increased to 60° C. Another set ofhighly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDSat 65° C. An additional set of highly stringent conditions are definedby hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC,0.1% SDS followed by 0.1×SSC, 0.1% SDS.

Hybridization requires that the two nucleic acids contain complementarysequences, although depending on the stringency of the hybridization,mismatches between bases are possible. The appropriate stringency forhybridizing nucleic acids depends on the length of the nucleic acids andthe degree of complementation, variables well known in the art. Thegreater the degree of similarity or homology between two nucleotidesequences, the greater the value of Tm for hybrids of nucleic acidshaving those sequences. The relative stability (corresponding to higherTm) of nucleic acid hybridizations decreases in the following order:RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotidesin length, equations for calculating Tm have been derived (see, e.g.,Maniatis at 9.50-9.51). For hybridizations with shorter nucleic acids,i.e., oligonucleotides, the position of mismatches becomes moreimportant, and the length of the oligonucleotide determines itsspecificity (see, e.g., Maniatis, at 11.7-11.8). In one embodiment thelength for a hybridizable nucleic acid is at least about 10 nucleotides.Preferably a minimum length for a hybridizable nucleic acid is at leastabout 15 nucleotides; more preferably at least about 20 nucleotides; andmost preferably the length is at least 30 nucleotides. Furthermore, theskilled artisan will recognize that the temperature and wash solutionsalt concentration can be adjusted as necessary according to factorssuch as length of the probe.

As used herein the term “codon-optimized” means that a nucleic acidcoding region has been adapted for expression in the cells of a givenorganism by replacing one, or more than one, or a significant number, ofcodons with one or more codons that are more frequently used in thegenes of that organism.

The term “percent identity”, as known in the art, is a relationshipbetween two or more polypeptide sequences or two or more polynucleotidesequences, as determined by comparing the sequences. In the art,“identity” also means the degree of sequence relatedness betweenpolypeptide or polynucleotide sequences, as the case can be, asdetermined by the match between strings of such sequences.

As known in the art, “similarity” between two polypeptides is determinedby comparing the amino acid sequence and conserved amino acidsubstitutes thereto of the polypeptide to the sequence of a secondpolypeptide. Similarity can be between two full sequences, or between afragment of one sequence and a fragment of a second sequence wherein thefragments are of comparable length or size, or between a fragment of onesequence and the entirety of a second sequence.

“Identity” and “similarity” can be readily calculated by known methods,including but not limited to those described in: Computational MolecularBiology (Lesk, A. M, ed.) Oxford University Press, N Y (1988);Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.)Academic Press, N Y (1993); Computer Analysis of Sequence Data, Part I(Griffin, A. M., and Griffin, H. G., eds.) Humana Press, N J (1994);Sequence Analysis in Molecular Biology (von Heinje, G., ed.) AcademicPress (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux,J., eds.) Stockton Press, NY (1991). Preferred methods to determineidentity are designed to give the best match between the sequencestested. Methods to determine identity and similarity are codified inpublicly available computer programs. Sequence alignments and percentidentity calculations can be performed using the Megalign program of theLASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.).Multiple alignments of the sequences disclosed herein were performedusing the Clustal method of alignment (Higgins and Sharp (1989) CABIOS.5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTHPENALTY=10). Default parameters for pairwise alignments using theClustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALSSAVED=5.

Suitable nucleic acid sequences or fragments thereof (isolatedpolynucleotides of the present invention) encode polypeptides that areat least about 70% to about 75% identical to the amino acid sequencesreported herein, at least about 80%, at least about 85%, at least about86%, at least about 87%, at least about 88%, at least about 89%, or atleast about 90% identical to the amino acid sequences reported herein,at least about 91%, at least about 92%, at least about 93%, at leastabout 94%, or at least about 95% identical to the amino acid sequencesreported herein, or at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or about 100% identical to the amino acidsequences reported herein. Suitable nucleic acid fragments are at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 76%, at leastabout 77%, at least about 78%, at least about 79%, at least about 80%,at least about 81%, at least about 82%, at least about 83%, at leastabout 84%, at least about 85%, at least about 86%, at least about 87%,at least about 88%, at least about 89%, at least about 90%, at leastabout 91%, at least about 92%, at least about 93%, at least about 94%,at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or about 100% identical to the nucleicacid sequences reported herein. Suitable nucleic acid fragments not onlyhave the above identities/similarities but typically encode apolypeptide having at least 50 amino acids, at least 100 amino acids, atleast 150 amino acids, at least 200 amino acids, or at least 250 aminoacids.

A DNA or RNA “coding region” is a DNA or RNA molecule which istranscribed and/or translated into a polypeptide in a cell in vitro orin vivo when placed under the control of appropriate regulatorysequences. “Suitable regulatory regions” refer to nucleic acid regionslocated upstream (5′ non-coding sequences), within, or downstream (3′non-coding sequences) of a coding region, and which influence thetranscription, RNA processing or stability, or translation of theassociated coding region. Regulatory regions include promoters,translation leader sequences, RNA processing site, effector binding siteand stem-loop structure. The boundaries of the coding region aredetermined by a start codon at the 5′ (amino) terminus and a translationstop codon at the 3′ (carboxyl) terminus. A coding region can include,but is not limited to, prokaryotic regions, cDNA from mRNA, genomic DNAmolecules, synthetic DNA molecules, or RNA molecules. If the codingregion is intended for expression in a eukaryotic cell, apolyadenylation signal and transcription termination sequence willusually be located 3′ to the coding region.

An “isoform” is a protein that has the same function as another proteinbut which is encoded by a different gene and can have small differencesin its sequence.

A “paralogue” is a protein encoded by a gene related by duplicationwithin a genome.

An “orthologue” is gene from a different species that has evolved from acommon ancestral gene by speciation. Normally, orthologues retain thesame function in the course of evolution as the ancestral gene.

“Open reading frame” is abbreviated ORF and means a length of nucleicacid, either DNA, cDNA or RNA, that comprises a translation start signalor initiation codon, such as an ATG or AUG, and a termination codon andcan be potentially translated into a polypeptide sequence.

“Promoter” refers to a DNA fragment capable of controlling theexpression of a coding sequence or functional RNA. In general, a codingregion is located 3′ to a promoter. Promoters can be isolated in theirentirety from a native gene, or be composed of different elementsderived from different promoters found in nature, or even comprisesynthetic DNA segments. It is understood by those skilled in the artthat different promoters can direct the expression of a gene indifferent tissues or cell types, or at different stages of development,or in response to different environmental or physiological conditions.Promoters which cause a gene to be expressed in most cell types at mosttimes are commonly referred to as “constitutive promoters”. It isfurther recognized that since in most cases the exact boundaries ofregulatory sequences have not been completely defined, DNA fragments ofdifferent lengths can have identical promoter activity. A promoter isgenerally bounded at its 3′ terminus by the transcription initiationsite and extends upstream (5′ direction) to include the minimum numberof bases or elements necessary to initiate transcription at levelsdetectable above background. Within the promoter will be found atranscription initiation site (conveniently defined for example, bymapping with nuclease SI), as well as protein binding domains (consensussequences) responsible for the binding of RNA polymerase. Severalpromoters are specifically identified by the present invention, however,one having ordinary skill in the art would understand that any number ofadditional promoters capable of driving the expression in yeast would beincluded in the present invention.

The term “linker” as used herein refers to a series of nucleotides oramino acids that connect one section of the chimeric polynucleotide orpolypeptide to another section of the chimeric polynucleotide ofpolypeptide. In some embodiments, the linker serves a structuralfunction.

A coding region is “under the control” of transcriptional andtranslational control elements in a cell when RNA polymerase transcribesthe coding region into mRNA, which is then trans-RNA spliced (if thecoding region contains introns) and translated into the protein encodedby the coding region.

“Transcriptional and translational control regions” are DNA regulatoryregions, such as promoters, enhancers, terminators, and the like, thatprovide for the expression of a coding region in a host cell. Ineukaryotic cells, polyadenylation signals are control regions.

As used herein the term “N-terminal region” refers to the portion of theamino acid sequence consisting of the most N-terminal amino acid residueup to the amino acid residue at position n/2, wherein n is the totalnumber of residues in the sequence. As used herein the term “C-terminalregion” refers to the portion of the amino acid sequence consisting ofthe most C-terminal amino acid residue up to the amino acid residue atposition n/2, wherein n is the total number of residues in the sequence.

The term “operably associated” refers to the association of nucleic acidsequences on a single nucleic acid fragment so that the function of oneis affected by the other. For example, a promoter is operably associatedwith a coding region when it is capable of affecting the expression ofthat coding region (i.e., that the coding region is under thetranscriptional control of the promoter). Coding regions can be operablyassociated to regulatory regions in sense or antisense orientation.

The term “expression,” as used herein, refers to the transcription andstable accumulation of sense (mRNA) or antisense RNA derived from thenucleic acid fragment of the invention. Expression can also refer totranslation of mRNA into a polypeptide.

The term “lignocellulose” refers to material that is comprised of ligninand cellulose. Examples of lignocelluloses are provided herein and areknown in the art. Examples of lignocellulosic materials include but arenot limited to corn stover, straw, bagasse, switchgrass, paper, andwood.

The “pentose phosphate pathway” or “PPP” refers to a biochemical pathwaythat creates NADPH from glucose-6-P. The PPP has both an oxidative phaseand a non-oxidative phase. There are several enzymes that have beenidentified to play a role in the PPP, including but not limited toglucose-6-P dehydrogenase, gluconolactonase, 6-phosphogluconatedehydrogenase, ribulose-5-phosphate isomerase, ribose-5-phosphateketol-isomerase (RKI1), ribulose-5-phosphate 3-epimerase (RPE1),transketolase (TKL1), and transaldolase (TAL1).

As used herein “xylose isomerase activity” refers to the ability of anenzyme to directly convert xylose to xylulose. A “xylose isomerase” or“XI” as used herein refers to a protein having xylose isomerase activity(EC 5.3.1.5).

The term “chimeric” or “chimera” refers to a polynucleotide orpolypeptide having a nucleotide or polypeptide sequence derived from twoor more distinct parent sequences. A “parent sequence” or “donorsequence” is a nucleotide or amino acid sequence used as a sourcesequence to create the chimeric polynucleotide or polypeptide.

As used herein the term “XYM1” or “XYM2” refers to a xylose isomerasecoding sequence or polypeptide isolated from an uncultured bacterium asdescribed by Parachin and Gorwa-Grauslund, “Isolation of xyloseisomerase by sequence- and function-based screening from a soilmetagenome library,” Biotechnology Biofuels 4(49 (2011).

As used herein, the term “anaerobic” refers to an organism, biochemicalreaction, or process that is active or occurs under conditions of anabsence of gaseous 0₂.

“Anaerobic conditions” are defined as conditions under which the oxygenconcentration in the fermentation medium is too low for themicroorganism to use it as a terminal electron acceptor. Anaerobicconditions can be achieved by sparging a fermentation medium with aninert gas such as nitrogen until oxygen is no longer available to themicroorganism as a terminal electron acceptor. Alternatively, anaerobicconditions can be achieved by the microorganism consuming the availableoxygen of fermentation until oxygen is unavailable to the microorganismas a terminal electron acceptor.

“Aerobic metabolism” refers to a biochemical process in which oxygen isused as a terminal electron acceptor to convert energy, typically in theform of ATP, from carbohydrates. Aerobic metabolism typically occurs,for example, via the electron transport chain in mitochondria ineukaryotes, wherein a single glucose molecule is metabolized completelyinto carbon dioxide in the presence of oxygen.

In contrast, “anaerobic metabolism” refers to a biochemical process inwhich oxygen is not the final acceptor of electrons generated. Anaerobicmetabolism can be divided into anaerobic respiration, in which compoundsother than oxygen serve as the terminal electron acceptor, and substratelevel phosphorylation, in which no exogenous electron acceptor is usedand products of an intermediate oxidation state are generated via a“fermentative pathway.”

In “fermentative pathways”, the amount of NAD(P)H generated byglycolysis is balanced by the consumption of the same amount of NAD(P)Hin subsequent steps. For example, in one of the fermentative pathways ofcertain yeast strains, NAD(P)H generated through glycolysis donates itselectrons to acetaldehyde, yielding ethanol. Fermentative pathways areusually active under anaerobic conditions but can also occur underaerobic conditions, under conditions where NADH is not fully oxidizedvia the respiratory chain.

As used herein, the term “end-product” refers to a chemical compoundthat is not or cannot be used by a cell, and so is excreted or allowedto diffuse into the extracellular environment. Common examples ofend-products from anaerobic fermentation include, but are not limitedto, ethanol, acetic acid, formic acid, lactic acid, hydrogen, and carbondioxide.

As used herein, “cofactors” are compounds involved in biochemicalreactions that are recycled within the cells and remain at approximatelysteady state levels. Common examples of cofactors involved in anaerobicfermentation include, but are not limited to, NAD⁺ and NADP⁺. Inmetabolism, a cofactor can act in oxidation-reduction reactions toaccept or donate electrons. When organic compounds are broken down byoxidation in metabolism, their energy can be transferred to NAD⁺ by itsreduction to NADH, to NADP⁺ by its reduction to NADPH, or to anothercofactor, FAD⁺, by its reduction to FADH₂. The reduced cofactors canthen be used as a substrate for a reductase.

As used herein, a “pathway” is a group of biochemical reactions thattogether can convert one compound into another compound in a step-wiseprocess. A product of the first step in a pathway can be a substrate forthe second step, and a product of the second step can be a substrate forthe third, and so on. Pathways of the present invention include, but arenot limited to, the pentose phosphate pathway, the xylose utilizationpathway, the ethanol production pathway, and the glycerol productionpathway. The term “recombination” or “recombinant” refers to thephysical exchange of DNA between two identical (homologous), or nearlyidentical, DNA molecules. Recombination can be used for targeted genedeletion or to modify the sequence of a gene. The terms “recombinantmicroorganism” and “recombinant host cell” are used interchangeablyherein and refer to microorganisms that have been genetically modifiedto express or over-express endogenous polynucleotides, or to expressheterologous polynucleotides, such as those included in a vector, orwhich have a modification in expression of an endogenous gene.

By “expression modification” it is meant that the expression of thegene, or level of a RNA molecule or equivalent RNA molecules encodingone or more polypeptides or polypeptide subunits, or activity of one ormore polypeptides or polypeptide subunits is up regulated ordown-regulated, such that expression, level, or activity, is greaterthan or less than that observed in the absence of the modification.

The term “iron metabolism” refers to the process by which a cellregulates the intracellular level of iron. The term “protein associatedwith iron metabolism” refers to a protein involved in the regulation ofintracellular iron, including, e.g., a protein that imports, exports,binds, and/or sequesters iron or a protein that controls the expressionof a gene that encodes for a protein that imports, exports, binds,and/or sequesters iron. The term “Fe/S cluster biosynthesis” refers tothe biosynthesis of Fe/S clusters, including, e.g., the assembly andloading of Fe/S clusters. The term “Fe/S cluster biosynthesis genes”,“Fe/S cluster biosynthesis proteins” or “Fe/S cluster biosynthesispathway” refers to those polynucleotides and/or genes that are involvedin the biosynthesis of Fe/S clusters, including, e.g., the assembly andloading of Fe/S clusters.

In one aspect of the invention, genes or particular polynucleotidesequences are partially, substantially, or completely deleted, silenced,inactivated, or down-regulated in order to inactivate the enzymaticactivity they encode. Complete deletions provide maximum stabilitybecause there is no opportunity for a reverse mutation to restorefunction. Alternatively, genes can be partially, substantially, orcompletely deleted, silenced, inactivated, or down-regulated byinsertion, deletion, removal, or substitution of nucleic acid sequencesthat disrupt the function and/or expression of the gene.

II. Xylose Isomerase Polypeptides

The present invention provides host cells comprising (a) one or moremutations in one or more endogenous genes encoding a protein associatedwith iron metabolism and (b) at least one gene encoding a polypeptidehaving xylose isomerase activity the use thereof. In some embodiments,the host cell heterologously expresses the polypeptide. In someembodiments, the heterologously expressed polypeptide is a naturallyoccurring polypeptide. In some embodiments, the heterologously expressedpolypeptide is recombinant. In some embodiments, the heterologouslyexpressed polypeptide is a chimeric polypeptide.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with any one of SEQ ID NOs: 1, 3, 5, 7, 9,11, 13, 15, 17, 19, 21, 23, 25, and/or 27. In some embodiments, thepolypeptide has an amino acid sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11,13, 15, 17, 19, 21, 23, 25, or 27. In some embodiments, the polypeptideis encoded by a polynucleotide sequence having at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least76%, at least 77%, at least 78%, at least 79%, at least 80%, at least81%, at least 82%, at least 83%, at least 84%, at least 85%, at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, or at least 99% sequence identity withany one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26,and/or 28. In some embodiments, the polypeptide is encoded by apolynucleotide sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18,20, 22, 24, 26, or 28. In some embodiments, the polypeptide has an aminoacid sequence having at least 80%, at least 85%, at least 86%, at least87%, at least 88%, at least 89%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% sequence identity with any one of SEQID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39,and/or 41. In some embodiments, the polypeptide has an amino acidsequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, or 41. In some embodiments, the polypeptide is encodedby a polynucleotide sequence having at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 76%, at least77%, at least 78%, at least 79%, at least 80%, at least 81%, at least82%, at least 83%, at least 84%, at least 85%, at least 86%, at least87%, at least 88%, at least 89%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% sequence identity with any one of SEQID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40,and/or 42. In some embodiments, the polypeptide is encoded by apolynucleotide sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18,20, 22, 24, 26, 28, 36, 38, 40, or 42.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ IDNO: 1. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:1.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:3. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:3.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:5. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:5.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:7. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:7.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:9. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:9.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:11. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:11.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:13. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:13.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:15. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:15.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:17. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:17.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:19. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:19.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:21. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:21.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:23. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:23.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:25. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:25.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:27. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:27.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:35. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:35.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:37. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:37.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:39. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:39.

In some embodiments, the polypeptide has an amino acid sequence havingat least 80%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the amino acid sequence of SEQ ID NO:41. In some embodiments, the polypeptide has an amino acid sequencehaving 100% sequence identity with the amino acid sequence of SEQ ID NO:41.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:2. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 2.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:4.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:6. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 6.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:8. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 8.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:10. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 10.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:12. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 12.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:14. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 14.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:16. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 16.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:18. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 18.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:20. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 20.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:22. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 22.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:24. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 24.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:26. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 26.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:28. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 28.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:36. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 36.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:38. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 38.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:40. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 40.

In some embodiments, the polypeptide is encoded by a polynucleotidesequence having at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 76%, at least 77%, at least 78%, atleast 79%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or atleast 99% sequence identity with the nucleotide sequence of SEQ ID NO:42. In some embodiments, the polypeptide is encoded by a polynucleotidesequence of SEQ ID NO: 42.

The present invention involves the heterologous expression of one ormore polypeptides having xylose isomerase activity. It is understood byone of ordinary skill in the art that any polypeptide having xyloseisomerase activity or any polynucleotide encoding such a polypeptide maybe used according to the present invention. Accordingly, this inventionis not limited to the list of example xylose isomerase polypeptidesprovided. It is understood that nucleotide sequences encoding any of thepolypeptides defined above are expressly included in the presentinvention. Further, any nucleotide sequence that comprises one or moreamino acid substitutions, insertions and/or deletions, but that arewithin the ranges of identity or similarity as defined herein areexpressly included in the invention. However, the polypeptides havingxylose isomerase activity share certain conserved motifs. In oneembodiment, the nucleotide sequence of the invention encodes a xyloseisomerase amino acid sequence comprising a xylose isomerase signaturesequence as defined, e.g., by Meaden et al. (1994, Gene, 141: 97-101):VXW[GP]GREG[YSTA] (present at positions 188-196, relative to SEQ ID NO:11) and [LIVM]EPKPX[EQ]P (present at positions 233-240, relative to SEQID NO: 11), wherein “X” can be any amino acid and wherein amino acids inbrackets indicates that one of the bracketed amino acids can be presentat that position in the signature sequence. A xylose isomerase aminoacid sequence of the invention can further comprise the conserved aminoacid residues His-103, Asp-106, and Asp-341, which constitute a triaddirectly involved in catalysis, Lys-236 plays a structural as well as afunctional catalytic role, and Glu-234 (relative to SEQ ID NO: 11),which is involved in magnesium binding (Vangrysperre et al.,“Localization of the essential histidine and carboxylate group inD-xylose isomerases,” Biochem. J. 265: 699-705(1990); Henrick et al.,“Structures of D-xylose isomerase from Arthrobacter strain B3728containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 Aresolution, respectively,” J. Mol. Biol. 208: 129-157 (1989); Bhosale etal., “Molecular and industrial aspects of glucose isomerase,” Microbiol.Rev. 60: 280-300 (1996)). Amino acid positions of the above signaturesequences and conserved residues refer to positions in the referenceamino acid sequence of the B. thetaiotaomicron xylose isomerase of SEQID NO: 11. In amino acid sequences of the invention other than SEQ IDNO: 11, the amino acid positions of one or more of the above signaturesequences and conserved residues are present in amino acid positionscorresponding to the positions of the signature sequences and conservedresidues in SEQ ID NO: 11, for example in a ClustalW (1.83 or 1.81)sequence alignment using default settings. The skilled person will knowhow to identify corresponding amino acid positions in xylose isomeraseamino acid sequences other than SEQ ID NO: 11 using amino acid sequencealignment algorithms as defined hereinabove. These regions and positionswill tolerate no or only conservative amino acid substitutions. Onehaving ordinary skill in the art would understand that even conservedmotifs can remain functional with conservative amino acid substitutions,and such substitutions are envisioned by the present invention. Aminoacid substitutions outside of these regions and positions are unlikelyto greatly affect xylose isomerase activity.

Additional structural features common to XIs have been described, e.g.,by Chang et al., “Crystal Structures of Thermostable Xylose Isomerasesfrom Thermus caldophilus and Thermus thermophiles: Possible StructuralDeterminants of Thermostability,” J. Mol. Biol. 288:623-34 (1999), whichis incorporated by reference in its entirety, and RCSB Protein DataBank, “Xylose Isomerase From Thermotoga neapolitana,”http://www.rcsb.org/pdb/explore/explore.do?structureId=1A0E, lastaccessed Jun. 29, 2014, at 5:15 pm. There are several known metalbinding sits in the XI sequence, including at residues Glu-234, Glu-270,His-273, Asp-298, Asp-309, Asp-311, and Asp-341. One having ordinaryskill in the art would understand that any deletions or non-conservativesubstitutions at any one or more of these residues may lead to adecreased functionability of the resulting XI.

In some embodiments, a host cell is engineered to express one or more ofthe xylose isomerase polypeptides. In some embodiments, the host cell isa fungal cell, e.g. a yeast cell, e.g. a S. cerevisiae cell. In someembodiments the host cell is modified to have mutations affecting atleast one gene encoding a protein of the pentose phosphate pathway. Insome embodiments, the host cell has at least one mutation affecting theexpression of at least one of XKS1, RKI1, RPE1, TKL1, TAL1, or acombination thereof. In some embodiments, the host cell has one or moremutations that correlate with an increase in the expression or anup-regulation of one or more of XKS1, RKI1, RPE1, TKL1, and/or TAL1. Insome embodiments the host cell can be modified through the heterologousexpression of one or more polynucleotides encoding XKS1, RKI1, RPE1,TKL1, and/or TAL1. In some embodiments, the host cell has one or moremutations that correlate with a decrease in the expression ordown-regulation of one or more of XKS1, RKI1, RPE1, TKL1, and/or TAL1.In some embodiments, the host cell has a modification of an endogenousaldose reductase. In some embodiments, the aldose reductase is GRE3. Insome embodiments, the host cell has a deletion or disruption of all orpart of the endogenous GRE3 gene. In some embodiments, the aldosereductase gene is YPR1. In some embodiments, the host cell has adeletion or disruption of all or part of the endogenous YPR1 gene. Insome embodiments, the host cell has a deletion or disruption of all orpart of both the endogenous GRE3 gene and the endogenous YPR1 gene. Insome embodiments, the host cell has a modification of PGM1 and/or PGM2.In some embodiments, the host cell overexpresses PGM1 and/or PGM2. Insome embodiments, the host cell has increased levels of Pgm1 and/or Pgm2polypeptide and/or mRNA relative to a comparable host cell lacking amodification of PGM1 and/or PGM2. In some embodiments, the host cell isa modified industrial yeast strain.

In some embodiments, the host cell comprises a deletion or disruption ofone or more native enzymes that function to produce glycerol and/orregulate glycerol synthesis as described in, e.g., U.S. PatentApplication Publication No. 2014/0186930, which is incorporated byreference herein in its entirety. In some embodiments, the host cellproduces less glycerol than a control recombinant microorganism withoutdeletion or disruption of said one or more endogenous enzymes thatfunction to produce glycerol and/or regulate glycerol synthesis. In someembodiments, the one or more endogenous enzymes that function to produceglycerol are encoded by a GPD1 polynucleotide, a GPD2 polynucleotide, orboth a GPD1 polynucleotide and a GPD2 polynucleotide. In someembodiments, one or both of the endogenous GPD1 and/or GPD2 genes aremodified by mutation or deletion. In some embodiments, the host cellcomprises a heterologous ADHE sequence. In some embodiments, theheterologous ADHE is from Bifidobacterium adolescentis. In someembodiments the native STL1 gene is upregulated by either modifying thepromoter of the native copies or by introducing additional copies ofSTL1. In some embodiments the host cell comprises an ortholog of thenative STL1. In some embodiments the native ACS2 gene is upregulated byeither modifying the promoter of the native copies or by introducingadditional copies of ACS2. In some embodiments the host cell comprisesan ortholog of the native ACS2 or ACS1 gene.

In some embodiments, the host cell comprises one or more mutations inone or more endogenous genes encoding a protein associated with ironmetabolism. In some embodiments, the host cell comprises one or moremutations in one or more endogenous genes encoding an iron uptakeprotein, iron utilization protein, and/or an iron/sulfur (Fe/S) clusterbiosynthesis protein. In some embodiments, the host cell comprises oneor more mutations in one or more endogenous genes encoding a polypeptideaffecting iron metabolism or Fe/S cluster biosynthesis. In someembodiments, the host cell is a recombinant yeast cell. In someembodiments, the recombinant yeast cell comprises one or more mutationsin one or more of an endogenous gene selected from the group ISU1, YFH1,NFS1, AFT1, AFT2, YAP5, FRA1, FRA2, GREX3, GREX4, CCC1, and combinationsthereof. In some embodiments, the recombinant yeast cell comprises oneor more mutations in one or more of an endogenous gene which ishomologous to one or more of an S. cerevisiae gene selected from thegroup ISU1, YFH1, NFS1, AFT1, AFT2, YAP5, FRA1, FRA2, GREX3, and GREX4.and CCC1. In some embodiments, the recombinant yeast cell comprises amutation in the endogenous AFT1 gene that results in iron-independentactivation of the iron regulon such as the AFT1-1^(up) or AFT2-1^(up)alleles (Rutherford et al., 2003). In some embodiments, the recombinantyeast cell comprises a deletion or disruption of YAP5 and/or CCC1 and/ora mutation in the endogenous AFT1 or AFT2 gene that results iniron-independent activation of the iron regulon such as the AFT1-1^(up)or AFT2-1^(up) alleles. In some embodiments, the host cell comprises oneor more mutations in one or more endogenous genes selected from FRA1,FRA2, GREX3, and GREX4, wherein the one or more mutations results inincreased Aft1 and/or Aft2 activity. In some embodiments, the increasedAft1 and/or Aft2 activity results in the increased expression of Aft1and/or Aft2 target genes. In some embodiments, the one or more mutationsin AFT1, AFT2, FRA1, FRA2, GREX3, and/or GREX4 prevent or limit AFT1and/or AFT2 from forming a complex with Grx3, Grx4, Fra1, and/or Fra2.

In some embodiments, the host cell expresses one or more heterologousgenes encoding a protein that is associated with iron metabolism. Insome embodiments, the heterologous gene confers on the recombinant yeastcell an increased ability to utilize xylose as compared to a similaryeast cell lacking the heterologous gene. In some embodiments, theheterologous gene is AFT1, AFT2, and/or an orthologue thereof. In someembodiments, the heterologous gene encodes a polypeptide having irontransport activity. In some embodiments, the heterologous gene encodes aprotein that increases the activity and/or expression of Aft1 and/orAft2. In some embodiments, the heterologous gene is a target of Aft1and/or Aft2. In some embodiments, the heterologous gene isconstitutively expressed. In some embodiments, the heterologous gene isoverexpressed. In some embodiments, the heterologous gene encodes aprotein that suppresses a gene or protein that suppresses Aft1 and/orAft2 activity and/or expression. In some embodiments, the heterologousgene encodes a protein that suppresses a gene or protein that suppressesthe activity and/or expression of one or more downstream targets of Aft1and/or Aft2.

In some embodiments, the host cell comprises one or more mutations inthe endogenous ISU1 gene that results in a polypeptide comprising atleast one amino acid substitution selected from the group consisting ofD71N, D71G, and S98F, wherein the position of the substitution isrelative to the amino acid positions of SEQ ID NO:29. In someembodiments, the host cell comprises one or more mutations in theendogenous YFH1 gene that results in a polypeptide comprising a T163Psubstitution, wherein the position of the substitution is relative tothe amino acid positions of SEQ ID NO:31. In some embodiments, the hostcell comprises one or more mutations in the endogenous NFS1 gene thatresults in a polypeptide comprising at least one amino acid substitutionselected from the group consisting of L115W and E458D, wherein theposition of the substitution is relative to the amino acid positions ofSEQ ID NO:33. In some embodiments, the host cell comprises a mutation inthe endogenous ISU1 gene that results in a polypeptide comprising theamino acid substitution D71N, wherein the position of the substitutionis relative to the amino acid positions of SEQ ID NO:29; and a mutationin the endogenous YFH1 gene that results in a polypeptide comprising theamino acid substitution T163P, wherein the position of the substitutionis relative to the amino acid positions of SEQ ID NO:31. In someembodiments, the mutation is homozygous. In some embodiments, themutation is heterozygous.

In some embodiments, the host cell comprises (a) one or more mutationsin one or more endogenous genes encoding a protein associated with ironmetabolism, iron uptake, iron utilization, and/or an iron/sulfur (Fe/S)cluster biosynthesis; and (b) at least one heterologous gene encoding apolypeptide having xylose isomerase activity. In some embodiments, atleast one heterologous polypeptide having xylose isomerase activity is axylose isomerase. One having skill in the art would understand that anynumber of known xylose isomerase sequences could be expressed in thehost cell of the present invention. In some embodiments the xyloseisomerase is a naturally occurring xylose isomerase. In someembodiments, the xylose isomerase is a recombinant polypeptide. In someembodiments, the xylose isomerase is a chimeric polypeptide. In someembodiments, the xylose isomerase is encoded by a nucleotide sequencethat has at least 80% sequence identity with a nucleotide sequenceselected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, and 28. In some embodiments, the xylose isomerase is encoded by anucleotide sequence that has at least 83% sequence identity with anucleotide sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14,16, 18, 20, 22, 24, 26, and 28. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 85%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28. In someembodiments, the xylose isomerase is encoded by a nucleotide sequencethat has at least 87% sequence identity with a nucleotide sequenceselected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, and 28. In some embodiments, the xylose isomerase is encoded by anucleotide sequence that has at least 90% sequence identity with anucleotide sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14,16, 18, 20, 22, 24, 26, and 28. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 91%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28. In someembodiments, the xylose isomerase is encoded by a nucleotide sequencethat has at least 92% sequence identity with a nucleotide sequenceselected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, and 28. In some embodiments, the xylose isomerase is encoded by anucleotide sequence that has at least 93% sequence identity with anucleotide sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14,16, 18, 20, 22, 24, 26, and 28. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 94%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28. In someembodiments, the xylose isomerase is encoded by a nucleotide sequencethat has at least 95% sequence identity with a nucleotide sequenceselected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, and 28. In some embodiments, the xylose isomerase is encoded by anucleotide sequence that has at least 96% sequence identity with anucleotide sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14,16, 18, 20, 22, 24, 26, and 28. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 97%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28. In someembodiments, the xylose isomerase is encoded by a nucleotide sequencethat has at least 98% sequence identity with a nucleotide sequenceselected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24,26, and 28. In some embodiments, the xylose isomerase is encoded by anucleotide sequence that has at least 99% sequence identity with anucleotide sequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14,16, 18, 20, 22, 24, 26, and 28. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 100%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28.

In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 80% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 83%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 85% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 87%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 90% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 91%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 92% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 93%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 94% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 95%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 96% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 97%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 98% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42. In some embodiments, the xyloseisomerase is encoded by a nucleotide sequence that has at least 99%sequence identity with a nucleotide sequence selected from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 36, 38, 40, and 42.In some embodiments, the xylose isomerase is encoded by a nucleotidesequence that has at least 100% sequence identity with a nucleotidesequence selected from SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 36, 38, 40, and 42.

In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 80% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,and 27. In some embodiments, the xylose isomerase has an amino acidsequence that has at least 83% sequence identity with an amino acidsequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19,21, 23, 25, and 27. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 85% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, and 27. In some embodiments, the xylose isomerasehas an amino acid sequence that has at least 87% sequence identity withan amino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13,15, 17, 19, 21, 23, 25, and 27. In some embodiments, the xyloseisomerase has an amino acid sequence that has at least 90% sequenceidentity with an amino acid sequence selected from SEQ ID NOs: 1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 91%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. In someembodiments, the xylose isomerase has an amino acid sequence that has atleast 92% sequence identity with an amino acid sequence selected fromSEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. Insome embodiments, the xylose isomerase has an amino acid sequence thathas at least 93% sequence identity with an amino acid sequence selectedfrom SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 94% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,and 27. In some embodiments, the xylose isomerase has an amino acidsequence that has at least 95% sequence identity with an amino acidsequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19,21, 23, 25, and 27. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 96% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, and 27. In some embodiments, the xylose isomerasehas an amino acid sequence that has at least 97% sequence identity withan amino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13,15, 17, 19, 21, 23, 25, and 27. In some embodiments, the xyloseisomerase has an amino acid sequence that has at least 98% sequenceidentity with an amino acid sequence selected from SEQ ID NOs: 1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 99%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. In someembodiments, the xylose isomerase has an amino acid sequence that has atleast 10% sequence identity with an amino acid sequence selected fromSEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 80% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, and 41. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 83% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, 27, 35, 37, 39, and 41. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 85%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 87% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, and 41. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 90% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, 27, 35, 37, 39, and 41. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 91%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 4143. In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 92% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, and 41. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 93% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, 27, 35, 37, 39, and 41. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 94%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 95% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, and 41. In some embodiments, the xylose isomerase has anamino acid sequence that has at least 96% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, 27, 35, 37, 39, and 41. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 97%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.In some embodiments, the xylose isomerase has an amino acid sequencethat has at least 98% sequence identity with an amino acid sequenceselected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 35, 37, 39, and 41 43. In some embodiments, the xylose isomerase hasan amino acid sequence that has at least 99% sequence identity with anamino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15,17, 19, 21, 23, 25, 27, 35, 37, 39, and 41. In some embodiments, thexylose isomerase has an amino acid sequence that has at least 10%sequence identity with an amino acid sequence selected from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

In some embodiments, the host cell comprises (a) one or mutation in theendogenous YFH1 gene that results in a polypeptide comprising a T163Psubstitution; and (b) at least one heterologous gene encoding apolypeptide having xylose isomerase activity, wherein the polypeptidehas an amino acid sequence at least about 80%, at least about 83%, atleast about 85%, at least about 87%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at about least98%, at about least 99%, or about 100% identical to the amino acidsequence of SEQ ID NO:1. In some embodiments, the host cell comprises(a) a deletion or disruption of GRE3 and/or YPR1; (b) one or moremutations that correlate with an increase in the expression orup-regulation of one or more of XKS1, RKI1, RPE1, TKL1, TAL1, PGM1and/or PGM2; (c) one or mutation in the endogenous YFH1 gene thatresults in a polypeptide comprising a T163P substitution; and (d) atleast one heterologous gene encoding a polypeptide having xyloseisomerase activity, wherein the polypeptide has an amino acid sequenceat least about 80%, at least about 83%, at least about 85%, at leastabout 87%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at about least 98%, at about least 99%,or about 100% identical to the amino acid sequence of SEQ ID NO:1. Insome embodiments, the host cell can be cultured in a medium supplementedwith iron. In some embodiments, the host cell can be cultured underconditions that facilitate and/or stimulate the uptake of iron by thehost cell. In some embodiments, the host cell can be cultured underconditions that hinder, prevent, block, and/or decrease the export ofiron from the host cell.

In some embodiments, the host cell comprises more than one copy of thepolynucleotide encoding the polypeptide having xylose isomeraseactivity. In some embodiments, the host cell comprises two copies, threecopies, four copies, five copies, six copies, seven copies, eightcopies, nine copies, ten copies, eleven copies, at least twelve copies,at least fifteen copies, or at least twenty copies of the polynucleotideencoding the polypeptide having xylose isomerase activity.

In some embodiments, the polynucleotide can be present in a vector. Insome embodiments, the host cell can comprise the polynucleotide within avector. In some embodiments, the vector is a plasmid. In someembodiments, the host cell can express the polynucleotide from thevector. In some embodiments, the polynucleotide can be incorporated intothe genome of the host cell. In some embodiments, the host cell is afungal cell. In some embodiments, the host cell is a yeast cell. In someembodiments, the host cell is a S. cerevisiae cell.

Certain embodiments of the present invention describe methods forproducing a fermentation product. In certain embodiments, therecombinant host cell comprising the polynucleotide or the polypeptideand a mutation in one or more genes encoding a protein associated withiron metabolism is contacted with a carbon source. In some embodiments,the host cell comprises a mutation in one or more genes encoding aprotein associated with iron metabolism, and the host cell is contactedwith a carbon source and an exogenous source of a polypeptide havingxylose isomerase activity. In certain embodiments, the carbon sourcecomprises xylose. In certain embodiments, xylose is the sole source ofcarbon in the carbon source. In certain embodiments, a fermentationproduct is produced by contacting the host cell with the carbon source.In certain embodiments, the fermentation product is recovered. Incertain embodiments, the fermentation product is selected from the groupconsisting of ethanol, lactic acid, 3-hydroxy-propionic acid, hydrogen,butyric acid, acrylic acid, acetic acid, succinic acid, citric acid,malic acid, fumaric acid, an amino acid, 1,3-propane-diol, ethylene,glycerol, acetone, isopropyl alcohol, butanol, a β-lactam, anantibiotic, cephalosporin, or a combination thereof. In certainembodiments, the fermentation product is ethanol.

IV. Codon-Optimization

In some embodiments, the nucleotide sequence of the one or morepolynucleotides disclosed in the present invention are codon-optimizedfor expression in a fungal host cell. In some embodiments, thenucleotide sequence of the polynucleotide is codon-optimized forexpression in a yeast host cell. In some embodiments the nucleotidesequence of the polynucleotide is codon-optimized for expression in S.cerevisiae. Codon-optimized polynucleotides can have a codon adaptationindex (CAI) of about 0.8 to 1.0, about 0.9 to 1.0, or about 0.95 to 1.0.

In general, highly expressed genes in an organism are biased towardscodons that are recognized by the most abundant tRNA species in thatorganism. One measure of this bias is the “codon adaptation index” or“CAI,” which measures the extent to which the codons used to encode eachamino acid in a particular gene are those which occur most frequently ina reference set of highly expressed genes from an organism. The CodonAdaptation Index is described in more detail in Sharp and Li, NucleicAcids Research 15:1281-1295 (1987), which is incorporated by referenceherein in its entirety.

The CAI of codon-optimized sequences used in the present inventioncorresponds to from about 0.6 to about 1.0, from about 0.7 to about 1.0,from about 0.8 to about 1.0, from about 0.9 to about 1.0, from about 9.5to about 1.0, or about 1.0. A codon-optimized sequence can be furthermodified for expression in a particular organism, depending on thatorganism's biological constraints. For example, large runs of “As” or“Ts” (e.g., runs greater than 4, 5, 6, 7, 8, 9, or 10 consecutive bases)can be removed from the sequences if these are known to effecttranscription negatively. Furthermore, specific restriction enzyme sitescan be removed for molecular cloning purposes. Examples of suchrestriction enzyme sites include Pad, Ascl, BamHI, BgIII, EcoRJ andXhol. Additionally, the DNA sequence can be checked for direct repeats,inverted repeats and mirror repeats with lengths of ten bases or longer,which can be modified manually by replacing codons with “second best”codons, i.e., codons that occur at the second highest frequency withinthe particular organism for which the sequence is being optimized.

Deviations in the nucleotide sequence that comprise the codons encodingthe amino acids of any polypeptide chain allow for variations in thesequence coding for the gene. Since each codon consists of threenucleotides, and the nucleotides comprising DNA are restricted to fourspecific bases, there are 64 possible combinations of nucleotides, 61 ofwhich encode amino acids (the remaining three codons encode signalsending translation). The “genetic code” which shows which codons encodewhich amino acids is well known to one of skill in the art. As a result,many amino acids are designated by more than one codon. For example, theamino acids alanine and proline are coded for by four triplets, serineand arginine by six, whereas tryptophan and methionine are coded by justone triplet. This degeneracy allows for DNA base composition to varyover a wide range without altering the amino acid sequence of theproteins encoded by the DNA.

Many organisms display a bias for use of particular codons to code forinsertion of a particular amino acid in a growing peptide chain. Codonpreference or codon bias, differences in codon usage between organisms,is afforded by degeneracy of the genetic code, and is well documentedamong many organisms. Codon bias often correlates with the efficiency oftranslation of messenger RNA (mRNA), which is in turn believed to bedependent on, inter alia, the properties of the codons being translatedand the availability of particular transfer RNA (tRNA) molecules. Thepredominance of selected tRNAs in a cell is generally a reflection ofthe codons used most frequently in peptide synthesis. Accordingly, genescan be tailored for optimal gene expression in a given organism based oncodon optimization.

Given the large number of gene sequences available for a wide variety ofanimal, plant and microbial species, it is possible to calculate therelative frequencies of codon usage. Codon usage tables andcodon-optimizing programs are readily available, for example, atwww.kazusa.or.jp/codon/ (visited Jul. 15, 2014), and these tables can beadapted in a number of ways. See, e.g., Nakamura, Y., et al. “Codonusage tabulated from the international DNA sequence databases: statusfor the year 2000,” Nucl. Acids Res. 28:292 (2000).

By utilizing one or more available tables, one of ordinary skill in theart can apply the frequencies to any given polypeptide sequence, andproduce a nucleic acid fragment of a codon-optimized coding region whichencodes the polypeptide, but which uses codons optimal for a givenspecies. Codon-optimized coding regions can be designed by variousdifferent methods known to one having ordinary skill in the art.

In certain embodiments, an entire polypeptide sequence, or fragment,variant, or derivative thereof is codon-optimized by any method known inthe art. Various desired fragments, variants or derivatives aredesigned, and each is then codon-optimized individually. In addition,partially codon-optimized coding regions of the present invention can bedesigned and constructed. For example, the invention includes a nucleicacid fragment of a codon-optimized coding region encoding a polypeptidein which at least about 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%of the codon positions have been codon-optimized for a given species.That is, they contain a codon that is preferentially used in the genesof a desired species, e.g., a yeast species such as S. cerevisiae, inplace of a codon that is normally used in the native nucleic acidsequence.

In additional embodiments, a full-length polypeptide sequence iscodon-optimized for a given species resulting in a codon-optimizedcoding region encoding the entire polypeptide, and then nucleic acidfragments of the codon-optimized coding region, which encode fragments,variants, and derivatives of the polypeptide are made from the originalcodon-optimized coding region. As would be well understood by those ofordinary skill in the art, if codons have been randomly assigned to thefull-length coding region based on their frequency of use in a givenspecies, nucleic acid fragments encoding fragments, variants, andderivatives would not necessarily be fully codon-optimized for the givenspecies. However, such sequences are still much closer to the codonusage of the desired species than the native codon usage. The advantageof this approach is that synthesizing codon-optimized nucleic acidfragments encoding each fragment, variant, and derivative of a givenpolypeptide, although routine, would be time consuming and would resultin significant expense.

In some embodiments, one or more of the donor parent polynucleotidesequences are codon-optimized for expression in yeast. In someembodiments, the chimeric polynucleotide is codon-optimized forexpression in yeast.

V. Methods of Producing Ethanol

Certain aspects of the present invention are directed to methods ofproducing a fermentation product. In some embodiments of the invention,the recombinant host cell is used to produce a fermentation product froma cellulosic or lignocellulosic material. In some embodiments, thefermentation product is ethanol, lactic acid, 3-hydroxy-propionic acid,hydrogen, butyric acid, acrylic acid, acetic acid, succinic acid, citricacid, malic acid, fumaric acid, an amino acid, 1,3-propane-diol,ethylene, glycerol, acetone, isopropyl alcohol, butanol, a β-lactam, anantibiotic, a cephalosporin, or a combination thereof. In someembodiments, the cellulosic or lignocellulosic material is insolublecellulose, crystalline cellulose, pretreated hardwood, paper sludge,pretreated corn stover, pretreated sugar cane bagasse, pretreated corncobs, pretreated switchgrass, pretreated municipal solid waste,pretreated distiller's dried grains, pretreated wheat straw, corn fiber,agave, or a combination thereof.

One aspect of the invention is directed to a composition comprising alignocellulosic material and a recombinant yeast host cell comprising atleast one polypeptide having xylose isomerase activity and comprising amutation in a gene encoding a protein associated with iron metabolism.Another aspect of the invention is directed to a media supernatantgenerated by incubating a recombinant yeast host comprising as least onepolypeptide having xylose isomerase activity and comprising a mutationin a gene encoding a protein associated with iron metabolism with amedium containing xylose as the only carbon source. In some embodiments,the medium comprises a cellulosic or lignocellulosic material. In someembodiments, the cellulosic or lignocellulosic material is insolublecellulose, crystalline cellulose, pretreated hardwood, paper sludge, sawmill or paper mill discards, pretreated corn stover, pretreated sugarcane bagasse, pretreated corn cobs, pretreated switchgrass, pretreatedmunicipal solid waste, pretreated distiller's dried grains, pretreatedwheat straw, corn fiber, agave, or a combination thereof.

In some embodiments, a fermentation product is produced by a methodcomprising contacting a recombinant host cell of the present inventionwith a carbon source, wherein the carbon source comprises xylose. Insome embodiments, the fermentation product is selected from the groupconsisting of ethanol, lactic acid, 3-hydroxy-propionic acid, hydrogen,butyric acid, acrylic acid, acetic acid, succinic acid, citric acid,malic acid, fumaric acid, an amino acid, 1,3-propane-diol, ethylene,glycerol, acetone, isopropyl alcohol, butanol, a β-lactam, anantibiotic, and a cephalosporin. In some embodiments, the fermentationproduct is ethanol. In some embodiments, the fermentation product isrecovered.

Certain aspects of the present invention are directed to a method ofproducing ethanol comprising contacting a source material comprisingxylose with a host cell of the present invention. In some embodimentsthe host cell heterologously expresses a polypeptide having xyloseisomerase activity. In some embodiments the host cell further comprisesa mutation in one or more genes encoding a polypeptide that isassociated with iron metabolism.

In some embodiments, the source material is a cellulosic biomass. Insome embodiments, the source material is a lignocellulosic biomass. Insome embodiments, the source material is selected from the groupconsisting of insoluble cellulose, crystalline cellulose, pretreatedhardwood, softwood, paper sludge, newspaper, sweet sorghum, pretreatedcorn stover, pretreated sugar cane bagasse, pretreated corn cobs,pretreated switchgrass, pretreated municipal solid waste, pretreateddistiller's dried grains, pretreated wheat straw, rice straw, nutshells, banana waste, sponge gourd fibers, corn fiber, agave, trees,corn stover, wheat straw, sugar cane bagasse, switchgrass, andcombinations thereof. In some embodiments, the source material is cornstover.

EXAMPLES

The invention now being generally described, it will be more readilyunderstood by reference to the following examples, which are includedmerely for purposes of illustration of certain aspect and embodiments ofthe present invention, and are not intended to limit the invention.

Example 1—S. cerevisiae Background Strain

A strain of S. cerevisiae was created that was suitable for the testingof functional xylose isomerases. The GRE3 locus of an industrial yeaststrain was replaced with expression cassettes for the pentose phosphatepathway genes RPE1, RKI1, TKL1, and TAL1 as well as the native S.cerevisiae xyulokinase XKS1 (FIG. 1).

Example 2—Identification of Iron Metabolism Related Genes Mutated inXylose Utilizing Strains

Specific mutations in three native S. cerevisiae genes (ISU1, YFH1, andNFS1) were identified that significantly improve performance of XIxylose engineered strains. The mutations were identified by reverseengineering several strains adapted for improved growth rate on xylosemedia. The adapted strains were derived from strains engineered toexpress an exogenous XI and to overexpress the native genes XKS, RKI1,RPE1, TAL1, and TKL1. Two strains were adapted that differed in thenative GRE3+ locus, with one strain having a deletion of the endogenousGRE3. The mutations can be directly engineered into a strain providingthe performance improvements usually obtained via adaptation. Thedirected engineering of these mutations saves the time and uncertaintyassociated with strain adaptations. These mutations can benefit strainsengineered with various XIs (see FIGS. 5 and 6).

Example 3—Mutations in YFH1, ISU1, and NFS1 Improve Growth on Xylose

Strains were grown on YPX media (yeast extract, peptone, and xylose)under anaerobic conditions in a Biotek plate reader. OD600 measurementswere used to determine changes in cell density over time (˜48 hrs) (FIG.3). Xylose Utilizing Strains (XUS) 1 and 2 are strains engineered toutilize xylose but without mutations in YFH1, ISU1, or NFS1. XUS1-1 andXUS1-2 strains were adapted for improved growth on xylose originatingfrom strain XUS1. Strain XUS2-1 was adapted for improved growth onxylose originating from strain XUS2. Genome sequencing revealedmutations in iron-sulfur cluster related genes in the adapted strainsXUS1-1 (YFH1), XUS1-2 (NFS1) and XUS2-1 (ISU1). Direct geneticengineering to revert the mutations to the wild type alleles(XUS1-1→YFH1 wt, XUS2-1→ISU1 wt, XUS1-2→NFS1 wt) decreased xylosegrowth, matching the original parent strains. Direct genetic engineeringof the iron-sulfur mutations into the parent strains (XUS1→YFH1 T163P,XUS2→ISU1 D71N, XUS1→NFS1 L115W) resulted in improved xylose growthmatching the adapted strains with the same parent and mutation. The ISU1D71N mutation was direct engineered as a heterozygote to match themutation found in the adapted strain XUS2-1.

Example 4—Homozygousing the ISU1^(D71N) Mutation Improves Growth onXylose

Strains were grown on YPX media (yeast extract, peptone, and xylose)under anaerobic conditions in a Biotek plate reader. OD600 measurementswere used to determine changes in cell density over time (˜48 hrs) (FIG.4A). The negative control is a strain that is unable to grow on xylose.Adapted strain XUS2-1 is heterozygous at the ISU1 locus. XUS2-1genetically engineered with two mutant alleles of ISU1^(D71N)(XUS2-1+ISU1* homo) exhibits improved growth on xylose relative to theoriginal heterozygote XUS2-1. Engineering the original parent strainwith two mutant alleles of ISU1^(D71N) (XUS2+ISU1* homo) results inimproved xylose growth equivalent to the XUS2-1ISU1^(D71N) homozygote.

Example 5—The Homozygous ISU1^(D71N) Mutation Improves Growth of theXUS1 GRE3⁺ Parent Strain

Strains were grown on YPX media (yeast extract, peptone, and xylose)under anaerobic conditions in a Biotek plate reader. OD600 measurementswere used to determine changes in cell density over time (˜48 hrs) (FIG.4B). The negative control is a strain that is unable to grow on xylose.The ISU1^(D71N) mutation was identified as a heterozygous mutation in anadapted xylose-utilizing strain with GRE3 deleted (XUS2-1). Directengineering of the ISU1^(D71N) heterozygous mutation into the GRE3⁺xylose strain XUS1 did not improve xylose growth (data not shown).Engineering XUS1 strain with two mutant alleles ofISU1^(D71N)(XUS1+ISU1* homo) results in significantly improved xylosegrowth equivalent to the XUS2 directly engineered ISU1^(D71N)homozygote(XUS2+ISU1* homo). Strain XUS1-1 is an adapted version of XUS1containing a homozygous mutation in YFH1. XUS1-1 directly engineeredhomozygous ISU1^(D71N) exhibits decreased performance.

Example 6—The YFH1^(T163P) Mutation Improves Growth of the Yeast StrainsHeterologously Expressing Various XIs

Strains were grown on YNBX minimal media, and the OD600 was measuredfollowing 48 hours of aerobic growth at 35° C. (FIG. 5). Various XIswere expressed on plasmids within the industrial host strain used forthe chimeric XI library (black bars) or the host strain plus the YFH1T163P Fe/Su cluster mutation (hashed bars). Eight colonies from eachtransformation were inoculated into YNBX media. Nearly all of the XIsthat generated growth above the negative control, which lacked an XI,showed a benefit from the presence of the YFH1 mutant allele.

In a second set of experiments, strains were grown on YPX media (yeastextract, peptone, xylose) under anaerobic conditions in a Biotek platereader at 35° C. OD600 measurements were used to determine changes incell density over time (˜48 hours) (FIGS. 6 A and B). The negativecontrol is a strain unable to grow on xylose. FIG. 6A shows strainscontaining the wild type allele of YFH1. FIG. 6B shows strainscontaining the YFH1T163P allele. All of the XIs tested using thisgenomic integration format showed significantly improved growth onxylose with the YFH1T163P allele present. CX355=chimeric xyloseisomerase 355, CX1224=chimeric xylose isomerase 1224, Ad=Abiotrophiadefectiva, Bt=Bacteroides thetaioatomicron, Pe=Piromyces,Ls=Lachnoanaerobaculum saburreum

Example 7—Mutations in AFT1 and CCC1 Improve Xylose Growth

Strains were grown on YPX media (yeast extract, peptone, and xylose)under anaerobic conditions in a Biotek plate reader. OD600 measurementswere used to determine changes in cell density over time (˜48 hrs) (FIG.7). The negative control is a strain that is unable to grow on xylose.Xylose utilizing strain (XUS) is a strain engineered to utilize xylose.XUS1-1 strain was adapted for improved growth on xylose originating fromstrain XUS1 and was found by genome sequencing to contain a mutation iniron-sulfur cluster related gene YFH1; XUS1-1 serves as a positivecontrol. Direct engineering of the AFT1-1UP allele into the XUS1 strain(XUS1+AFT1-1UP) slightly improved growth on xylose. Direct engineeringof the AFT1-1UP allele into and deletion of both endogenous copies ofCCC1 in the XUS1 strain (XUS1+AFT1-1UP, ccc1Δ) result in significantlyimproved xylose growth close to that of the XUS1-1 strain.

Example 8—Addition of Iron Improves Growth on Xylose

Strains were grown on SP1 media (yeast nitrogen base with amino acids,tri-sodium citrate, glucose, xylose) under anaerobic conditions in serumbottles. Samples were taken and measured for ethanol, xylose and glucoseconcentrations over time (˜65 hours) (FIG. 8). Xylose Utilizing Strain 2(XUS2) is engineered to utilize xylose. Strain XUS2-1 was adapted forimproved growth on xylose originating from XUS2. Genome sequencingrevealed mutations in iron-sulfur cluster related gene ISU1 in strainXUS2-1. Samples indicated as “+iron” were supplemented with iron at thestart of the fermentation. The strains consumed all of the glucose atsimilar rates during the first ˜18 hours of the fermentation andproduced similar amounts of ethanol with no difference seen with theaddition of iron. In contrast, the addition of iron significantlyimproved the rate of xylose utilization as seen in the increased ethanolproduction between 18 and 65 hours. The increased xylose utilization(and subsequent ethanol production) was seen for both strains with andwithout the mutations in the iron-sulfur cluster related genes.

Example 9—Iron Addition Enables Significant Activity of Xylose IsomeraseIn Vitro

Xylose isomerase functions as a tetramer with the binding of twodivalent cations per subunit essential for enzyme activity. Mg2+, Mn2+,Co2+, and Fe2+ ions activate the enzyme (Waltman et al. ProteinEngineering, Design & Selection, 2014, p. 1-6). Using an in vitroenzymatic assay, the addition of Fe2+ was found to result insignificantly more xylose isomerase activity than the addition of Mg2+(FIG. 9). The protocol was essentially the same as described in Zou etal (Metabolic Engineering. 14, 2012, p. 611-622) with the exception ofthe use of three different buffers for the assay which varied in theabsence or presence of the divalent metals Mg2+ or Fe2+. A cell extractwas made from strain XUS1 which expresses the Bacteroidesthetaiotaomicron xylose isomerase. The cell extract was combined withTris buffer+/− divalent metals, NADH, and sorbitol dehydrogenase. Theassay was initiated with the addition of xylose and the reaction wasmonitored for 2 minutes at 340 nm to determine the initial rate. Thereactions were performed under inert atmosphere and reducing conditionsto deter oxidation of Fe2+ to Fe3+. One unit of activity is equal to 1umol NADH oxidized/min/ml, which corresponds directly with theconsumption of the xylose that is added to initiate the reaction.

All documents cited herein, including journal articles or abstracts,published or corresponding U.S. or foreign patent applications, issuedor foreign patents, or any other documents, are each entirelyincorporated by reference herein, including all data, tables, figures,and text presented in the cited documents.

Following are particular embodiments of the disclosed invention

E1. A recombinant yeast cell comprising (a) at least one heterologousgene encoding a protein associated with iron metabolism and/or one ormore mutations in one or more endogenous gene encoding a proteinassociated with iron metabolism; and (b) at least one heterologous geneencoding a polypeptide having xylose isomerase activity.

E2. The recombinant yeast cell of E1, wherein the at least oneheterologous gene encoding a protein associated with iron metabolismand/or the one or more mutations in one or more endogenous gene encodinga protein associated with iron metabolism confers on the recombinantyeast cell an increased ability to utilize xylose as compared to asimilar yeast cell lacking the one or more mutations.

E3. The recombinant yeast cell of E1 or E2, wherein the one or moremutations is a heterozygous mutation.

E4. The recombinant yeast cell of E1 or E2, wherein the one or moremutations is a homozygous mutation.

E5. The recombinant yeast cell of any one of E1-E4, wherein therecombinant yeast cell is a member of a genus selected from the groupconsisting of Saccharomyces, Kluyveromyces, Candida, Pichia,Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, and Yarrowia.

E6. The recombinant yeast cell of claim E5, wherein the recombinantyeast cell is a member of a species selected from the group consistingof Saccharomyces cerevisiae, Saccharomyces bulderi, Saccharomycesexiguus, Saccharomyces uvarum, Saccharomyces diastaticus, Candidakrusei, Kloeckera lactis, Kloeckera marxianus, and Kloeckera fragilis.

E7. The recombinant yeast cell of claim E5, wherein the recombinantyeast cell is a member of a species selected from the group consistingof Saccharomyces cerevisiae, Saccharomyces bulderi, Saccharomycesexiguus, Saccharomyces uvarum, Saccharomyces diastaticus, Kloeckeralactis, Kloeckera marxianus, and Kloeckera fragilis.

E8. The recombinant yeast cell of any one of E1-E7, wherein therecombinant yeast cell is S. cerevisiae.

E9. The recombinant yeast cell of any one of E1-E4, wherein the one ormore mutations in an endogenous gene is in a gene selected from thegroup consisting of ISU1, YFH1, NFS1, AFT1, AFT2, YAP5, FRA1, FRA2,GREX3, GREX4, CCC1, and any combination thereof.

E10. The recombinant yeast cell of E9, wherein the one or more mutationsis a substitution of at least one nucleotide.

E11. The recombinant yeast cell of E10, wherein the recombinant yeastcell comprises one or more mutations in the endogenous ISU1 gene thatresults in a polypeptide comprising at least one amino acid substitutionselected from the group consisting of D71N, D71G, and S98F, wherein theposition of the substitution is relative to the amino acid positions ofSEQ ID NO:29.

E12. The recombinant yeast cell of E10 or E11, wherein the recombinantyeast cell comprises one or more mutations in the endogenous YFH1 genethat results in a polypeptide comprising a T163P substitution, whereinthe position of the substitution is relative to the amino acid positionsof SEQ ID NO:31.

E13. The recombinant yeast cell of any one of E10-E12, wherein therecombinant yeast cell comprises one or more mutations in the endogenousNFS1 gene that results in a polypeptide comprising at least one aminoacid substitution selected from the group consisting of L115W and E458D,wherein the position of the substitution is relative to the amino acidpositions of SEQ ID NO:33.

E14. The recombinant yeast cell of any one of E9-E13, wherein therecombinant yeast cell comprises a mutation in the endogenous AFT1 genethat results in increased Aft1 activity.

E15. The recombinant yeast cell of any one of E9-E14, wherein therecombinant yeast cell comprises a mutation in the endogenous AFT2 genethat results in increased Aft2 activity.

E16. The recombinant yeast cell of any one of E9-E15, wherein therecombinant yeast cell comprises one or more mutations in one or moreendogenous genes selected from FRA1, FRA2, GREX3, and GREX4; wherein theone or more mutations results in increased activity of Aft1 and/or Aft2;and/or wherein the one or more mutations results in increased expressionof one or more genes regulated by Aft1 and/or Aft2.

E17. The recombinant yeast cell of E16, wherein the recombinant yeastcell further comprises a mutation in an endogenous gene selected fromthe group consisting of YAP5 and CCC1.

E18. The recombinant yeast cell of E17, wherein the recombinant yeastcell comprises a deletion or disruption of YAP5 or CCC1.

E19. The recombinant yeast cell of any one of E1-E18, wherein theheterologous gene (a) is selected from the group consisting of AFT1,AFT2, and orthologues and combinations thereof.

E20. The recombinant yeast cell of any one of E1-E18, whereinheterologous gene (a) encodes a protein that increases the activity ofAft1 and/or Aft2 and/or increases the expression of AFT1 and/or AFT2.

E21. The recombinant yeast cell of E18, wherein the heterologous gene(a) encodes a protein that suppresses or inhibits the activity and/orexpression of a protein that suppresses or inhibits the activity of Aft1and/or Aft2 and/or suppresses or inhibits the expression of AFT1 and/orAFT2.

E22. The recombinant yeast cell of any one of E1-E18, wherein theheterologous gene (a) encodes a target of Aft1 and/or Aft2.

E23. The recombinant yeast cell of any one of E1-E18, wherein theheterologous gene (a) encodes a polypeptide having iron transportactivity.

E24. The recombinant yeast cell of any one of E1-E23, wherein theheterologous gene (a) is constitutively expressed.

E25. The recombinant yeast cell of any one of E1-E24, wherein theheterologous gene (b) encodes a xylose isomerase enzyme.

E26. The recombinant yeast cell of E25, wherein the heterologous gene(b) encodes a polypeptide having at least 80% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

E27. The recombinant yeast cell of E25, wherein the heterologous gene(b) encodes a polypeptide having at least 80% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

E28. The recombinant yeast cell of E26, wherein the heterologous gene(b) encodes a polypeptide having at least 85% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

E29. The recombinant yeast cell of E27, wherein the heterologous gene(b) encodes a polypeptide having at least 85% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

E30. The recombinant yeast cell of E28, wherein the heterologous gene(b) encodes a polypeptide having at least 90% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

E31. The recombinant yeast cell of E29, wherein the heterologous gene(b) encodes a polypeptide having at least 90% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

E32. The recombinant yeast cell of E30, wherein the heterologous gene(b) encodes a polypeptide having at least 95% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

E33. The recombinant yeast cell of E31, wherein the heterologous gene(b) encodes a polypeptide having at least 95% sequence identity with anamino acid sequence selected from the group consisting of SEQ ID NOs: 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

E34. The recombinant yeast cell of E32, wherein the heterologous gene(b) encodes a polypeptide having 100% sequence identity with an aminoacid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39, and 41.

E35. The recombinant yeast cell of E33, wherein the heterologous gene(b) encodes a polypeptide having 100% sequence identity with an aminoacid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5,7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27.

E36. The recombinant yeast cell of any one of E1-E35, wherein therecombinant yeast cell further comprises at least one geneticmodification of one or more endogenous genes encoding a protein of thepentose phosphate pathway.

E37. The recombinant yeast cell of E36, wherein the recombinant yeastcell comprises at least one genetic modification in at least one of theendogenous genes selected from the group consisting of XKS1, RKI1, RPE1,TKL1, and TAL1.

E38. The recombinant yeast cell of E37, wherein the recombinant yeastcell comprises one or more genetic modifications that leads to theoverexpression of at least one of the endogenous genes selected from thegroup consisting of XKS1, RKI1, RPE1, TKL1, and TAL1.

E39. The recombinant yeast cell of any one of E1-E38, wherein therecombinant yeast cell further comprises a deletion or disruption of oneor more aldose reductase genes.

E40. The recombinant yeast cell of E39, wherein the aldose reductasegene is GRE3 or YPR1.

E41. The recombinant yeast cell of E40, wherein the recombinant yeastcell comprises a deletion or disruption of GRE3 and YPR1.

E42. The recombinant yeast cell of any one of E1-E41, wherein the yeastcell further comprises a modification of the endogenous PGM1 gene.

E43. The recombinant yeast cell of E42, wherein the modification of theendogenous PGM1 gene results in the overexpression of PGM1.

E44. The recombinant yeast cell of any one of E1-E43, wherein therecombinant yeast cell is capable of growing on xylose as the solecarbon source.

E45. A method for producing a fermentation product comprising contactingthe recombinant yeast cell of any one of E1-E44 with a carbon source,wherein said carbon source comprises xylose and/or xylan.

E46. A method for producing a fermentation product comprising contactingthe recombinant yeast cell of any one of E1-E44 with a carbon source,wherein said carbon source comprises xylose.

E47. The method of E45, wherein the recombinant yeast cell is furthergrown on a media supplemented with iron.

E48. The method of E45 or E46, wherein the fermentation product isselected from the group consisting of ethanol, lactic acid,3-hydroxy-propionic acid, hydrogen, butyric acid, acrylic acid, aceticacid, succinic acid, citric acid, malic acid, fumaric acid, an aminoacid, 1,3-propane-diol, ethylene, glycerol, acetone, isopropyl alcohol,butanol, a β-lactam, an antibiotic, a cephalosporin, and combinationsthereof.

E49. The method of E47, wherein the fermentation product is ethanol.

E50. The method of any one of E45-E48, further comprising recovering thefermentation product.

E51. A method of producing ethanol comprising contacting a carbon sourcecomprising xylose and/or xylan with the recombinant yeast cell of anyone of E1-E44 in a fermentation medium under conditions wherein ethanolis produced.

E52. A method of producing ethanol comprising contacting a carbon sourcecomprising xylose with the recombinant yeast cell of any one of E1-E44in a fermentation medium under conditions wherein ethanol is produced.

E53. The method of E50, wherein the fermentation medium is supplementedwith iron.

E54. The method of E50 or E51, wherein the carbon source comprisescellulosic or lignocellulosic biomass.

E55. The method of E52, wherein the cellulosic or lignocellulosicbiomass is selected from the group consisting of insoluble cellulose,crystalline cellulose, pretreated hardwood, paper sludge, pretreatedcorn stover, pretreated sugar cane bagasse, pretreated corn cobs,pretreated switchgrass, pretreated municipal solid waste, pretreateddistiller's dried grains, pretreated wheat straw, corn fiber, agave,trees, corn stover, wheat straw, sugar cane bagasse, switchgrass, andcombinations thereof.

E56. The method of E53, wherein the biomass is corn stover.

E57. The method of claim any one of E50-E54, further comprisingrecovering the ethanol.

E58. The recombinant yeast cell of any one of E1-E44 for use in afermentation which convert a carbon source into a fermentation product,wherein said carbon source comprises xylose and/or xylan.

E59. The recombinant yeast cell of E35, wherein the recombinant yeastcell comprises heterologous expression of one or more polynucleotidesencoding XKS1, RKI1, RPE1, TKL1, and/or TAL1.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

The invention claimed is:
 1. A recombinant yeast cell comprising (a) atleast one heterologous gene encoding a protein associated with ironmetabolism and/or one or more mutations in one or more endogenous geneencoding a protein associated with iron metabolism; and (b) at least oneheterologous gene encoding a polypeptide having xylose isomeraseactivity; wherein the gene encoding a protein associated with ironmetabolism is YFH1.
 2. The recombinant yeast cell of claim 1, whereinthe YFH1 gene encodes a polypeptide having at least 80% sequenceidentity to SEQ ID NO: 31 and comprising a T163P substitution.
 3. Therecombinant yeast cell of claim 1, wherein the heterologous gene (b)encodes a polypeptide having at least 80%, 85%, 90%, 95% or 100%sequence identity with an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25,27, 29, 31, 33, 35, and
 37. 4. The recombinant yeast cell of claim 1,wherein the recombinant yeast cell further comprises at least onegenetic modification of one or more endogenous genes encoding a proteinof the pentose phosphate pathway.
 5. The recombinant yeast cell of claim4, wherein the recombinant yeast cell comprises at least one geneticmodification in at least one of the endogenous genes selected from thegroup consisting of XKS1, RKI1, RPE1, TKL1, and TAL1.
 6. The recombinantyeast cell of claim 5, wherein the recombinant yeast cell furthercomprises a deletion or disruption of one or more aldose reductasegenes.
 7. The recombinant yeast cell of claim 6, wherein the aldosereductase gene is GRE3 or YPR1.
 8. The recombinant yeast cell of claim7, wherein the yeast cell further comprises a modification of theendogenous PGM1 gene.
 9. The recombinant yeast cell of claim 1, whereinthe recombinant yeast cell comprises heterologous expression of one ormore polynucleotides encoding XKS1, RKI1, RPE1, TKL1, and/or TAL1. 10.The recombinant yeast cell of claim 1, wherein the at least oneheterologous gene encoding a protein associated with iron metabolismand/or the one or more mutations in one or more endogenous gene encodinga protein associated with iron metabolism confers on the recombinantyeast cell an increased ability to utilize xylose as compared to asimilar yeast cell lacking the one or more mutations.
 11. Therecombinant yeast cell of claim 1, wherein the recombinant yeast cell isa member of a genus selected from the group consisting of Saccharomyces,Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula,Kloeckera, Schwanniomyces, and Yarrowia.
 12. The recombinant yeast cellof claim 1, wherein the recombinant yeast cell is S. cerevisiae.
 13. Amethod for producing a fermentation product comprising contacting therecombinant yeast cell of claim 1 with a carbon source, wherein saidcarbon source comprises xylose and/or xylan.
 14. A method of claim 13,wherein the fermentation product is ethanol.
 15. A method for producinga fermentation product comprising contacting the recombinant yeast cellof claim 2 with a carbon source, wherein said carbon source comprisesxylose and/or xylan.
 16. A method of claim 15, wherein the fermentationproduct is ethanol.